[gmx-users] Re: trjconv for pbc

[rankinb]

Tsjerk,

Thanks for your reply.  I have tried using the center option, but ran into
similar problems.  Here are the exact commands that I used:

g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within
0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains
the water molecules and group 13 is the solute molecule)

trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875

trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center

Does this procedure seem reasonable?

Thanks,
Blake

--
View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012162.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.